Keep aware of how far the stem of the funnel protrudes: you don't want to clip something and snap it off (done that). Also, some solvent mixtures are more prone to emulsification than others (dichloromethane/water, for example). There are various tricks to remove emulsions, such as adding some brine, a very small amount of acetone, filtering through celite before attempting to separate, among others.
I tend not to agitate too vigorously, but enough to get efficient mixing. Repeated inversion and gentle shaking/swirling is usually sufficient Don't neglect to vent, especially with volatile solvents such as ether